AndersJing/SequenceEncoding

Protein Sequence Encoding

The python script to encode protein sequences using different encoding methods.

Requirements

• Python 2 or 3
  • json
  • argparse

Usage

./SequenceEncoding.py -seq="XXXXXX" [options]

positional arguments:

seq                   The protein sequence to be encoded.

optional arguments:

-h, --help            show this help message and exit
  
--encoding_type ENCODING_TYPE      
                      The encoding type. [One_hot, One_hot_6_bit,
                           Binary_5_bit, Hydrophobicity_matrix,
                           Meiler_parameters, Acthely_factors, PAM250, BLOSUM62,
                           Miyazawa_energies, Micheletti_potentials, AESNN3,
                           ANN4D, ProtVec]. 
                      Default: One_hot.
                    
--overlap             The word extraction strategy for ProtVec encoding: overlap.
                    
--non-overlap         The word extraction strategy for ProtVec encoding: non-overlap.

Reference

Xiaoyang Jing, Qiwen Dong, Daocheng Hong, Ruqian Lu. Amino acid encoding methods for protein sequence: a comprehensive review and assessment. Submitted, 2019.